I've selected all the interior holes, set cutting instructions, no problem.
Select all the outside faces, click "Apply", get this message:
I have done these operations on many designs and never had this problem. Seaching the forum, internet, etc yields no explanation of "list index out of range", likewise with the Area.cpp messages.<Path.Area> Area.cpp(1312): project failed
<Path.Area> Area.cpp(1454): empty projection
PathProfile.ERROR: Unable to create path for face(s).
list index out of range
I find it hard to imagine that there are too many faces selected (?), and can think of nothing else that is different between this object and others I've made.
Next step would be (to me) to select the pockets on the edge as one job, and the outer faces as the 3rd & final job.
File: